177 research outputs found
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Consistent Relationship between Field-Measured Stomatal Conductance and Theoretical Maximum Stomatal Conductance in C<sub>3</sub> Woody Angiosperms in Four Major Biomes
Premise of research. Understanding the relationship between field-measured operating stomatal conductance (gop) and theoretical maximum stomatal conductance (gmax), calculated from stomatal density and geometry, provides an important framework that can be used to infer leaf-level gas exchange of historical, herbarium, and fossil plants. To date, however, investigation of the nature of the relationship between gop and theoretical gmax remains limited to a small number of experiments on relatively few taxa and is virtually undefined for plants in natural ecosystems.
Methodology. We used the gop measurements of 74 species and 35 families across four biomes from a published contemporary data set of field-measured leaf-level stomatal conductance in woody angiosperms and calculated the theoretical gmax from the same leaves to investigate the relationship between gop and gmax across multiple species and biomes and determine whether such relationships are widely conserved.
Pivotal results. We observed significant relationships between gop and gmax, with consistency in the gop ∶ gmax ratio across biomes, growth habits (shrubs and trees), and habitats (open canopy and understory subcanopy). An overall mean gop ∶ gmax ratio of 0.26 ± 0.11 (mean ± SD) was observed. The consistently observed gop ∶ gmax ratio in this study strongly agrees with previous hypotheses that an ideal gop ∶ gmax ratio exists.
Conclusions. These results build substantially on previous studies by presenting a new reference for a consistent gop ∶ gmax ratio across many levels and offer great potential to enhance paleoclimate proxies and vegetation-climate models alike
ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data
BACKGROUND: ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. While several tools have been developed or adopted for assessing read quality, identifying nucleosome occupancy and accessible regions from ATAC-seq data, none of the tools provide a comprehensive set of functionalities for preprocessing and quality assessment of aligned ATAC-seq datasets.
RESULTS: We have developed a Bioconductor package, ATACseqQC, for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq data. In addition, this package contains functions to preprocess aligned ATAC-seq data for subsequent peak calling. Here we demonstrate the utilities of our package using 25 publicly available ATAC-seq datasets from four studies. We also provide guidelines on what the diagnostic plots should look like for an ideal ATAC-seq dataset.
CONCLUSIONS: This software package has been used successfully for preprocessing and assessing several in-house and public ATAC-seq datasets. Diagnostic plots generated by this package will facilitate the quality assessment of ATAC-seq data, and help researchers to evaluate their own ATAC-seq experiments as well as select high-quality ATAC-seq datasets from public repositories such as GEO to avoid generating hypotheses or drawing conclusions from low-quality ATAC-seq experiments. The software, source code, and documentation are freely available as a Bioconductor package at https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html
Rising CO<sub>2</sub> drives divergence in water use efficiency of evergreen and deciduous plants
Intrinsic water use efficiency (iWUE), defined as the ratio of photosynthesis to stomatal conductance, is a key variable in plant physiology and ecology. Yet, how rising atmospheric CO2 concentration affects iWUE at broad species and ecosystem scales is poorly understood. In a field-based study of 244 woody angiosperm species across eight biomes over the past 25 years of increasing atmospheric CO2 (~45 ppm), we show that iWUE in evergreen species has increased more rapidly than in deciduous species. Specifically, the difference in iWUE gain between evergreen and deciduous taxa diverges along a mean annual temperature gradient from tropical to boreal forests and follows similar observed trends in leaf functional traits such as leaf mass per area. Synthesis of multiple lines of evidence supports our findings. This study provides timely insights into the impact of Anthropocene climate change on forest ecosystems and will aid the development of next-generation trait-based vegetation models
Reproductive compatibility of a newly imported Australian population of the biocontrol agent Anaphes nitens with an existing South African population
Introductions of natural enemies in classical biocontrol programs potentially cause genetic bottlenecks which can be detrimental for biocontrol. This can be mitigated by introducing multiple populations of a natural enemy, but thorough pre-release testing is needed to ensure compatibility. In this study compatibility between an established population of Anaphes nitens in South Africa and a newly imported A. nitens population from Australia was tested. Anaphes nitens is an egg parasitoid of Gonipterus sp. n. 2, an important pest in Eucalyptus plantations. South African and Australian A. nitens lineages were compared to two admixed lineages, which were reared from the F0 to the F2 generation. No differences were found in the proportion of replicates producing offspring overall, or female offspring specifically, indicating there was no sexual isolation between the populations. The typical symptoms of cytoplasmic incompatibility in haplodiploids, namely male biased sex ratios, were not observed. The lack of significant differences in fecundity and development time between the lineages suggested that there was no hybrid vigour or outbreeding depression. We conclude that a field release of the imported A. nitens population poses a low risk of disrupting the existing biocontrol program due to reproductive barriers or outbreeding depression. Whether there is a benefit of adding the newly imported Australian A. nitens population to the existing biocontrol system in South Africa needs to be studied further, for example by performing a field release combined with post-release assessments for determining establishment and spread.https://www.elsevier.com/locate/ybconhj2024BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyZoology and EntomologySDG-15:Life on lan
Sympathy for the Devil: A Conservation Strategy for Devil and Manta Rays
Background International trade for luxury products, medicines, and tonics poses a threat to both terrestrial and marine wildlife. The demand for and consumption of gill plates (known as Peng Yu Sai, “Fish Gill of Mobulid Ray”) from devil and manta rays (subfamily Mobulinae, collectively referred to as mobulids) poses a significant threat to these marine fishes because of their extremely low productivity. The demand for these gill plates has driven an international trade supplied by largely unmonitored and unregulated catches from target and incidental fisheries around the world. Scientific research, conservation campaigns, and legal protections for devil rays have lagged behind those for manta rays despite similar threats across all mobulids.
Methods To investigate the difference in attention given to devil rays and manta rays, we examined trends in the scientific literature and updated species distribution maps for all mobulids. Using available information on target and incidental fisheries, and gathering information on fishing and trade regulations (at international, national, and territorial levels), we examined how threats and protective measures overlap with species distribution. We then used a species conservation planning approach to develop the Global Devil and Manta Ray Conservation Strategy, specifying a vision, goals, objectives, and actions to advance the knowledge and protection of both devil and manta rays.
Results and Discussion Our literature review revealed that there had been nearly 2.5-times more “manta”-titled publications, than “mobula” or “devil ray”-titled publications over the past 4.5 years (January 2012–June 2016). The majority of these recent publications were reports on occurrence of mobulid species. These publications contributed to updated Area of Occupancy and Extent of Occurrence maps which showed expanded distributions for most mobulid species and overlap between the two genera. While several international protections have recently expanded to include all mobulids, there remains a greater number of national, state, and territory-level protections for manta rays compared to devil rays. We hypothesize that there are fewer scientific publications and regulatory protections for devil rays due primarily to perceptions of charisma that favour manta rays. We suggest that the well-established species conservation framework used here offers an objective solution to close this gap. To advance the goals of the conservation strategy we highlight opportunities for parity in protection and suggest solutions to help reduce target and bycatch fisheries
Distribution of Gonipterus species and their egg parasitoids in Australia : implications for biological control
Gonipterus species are pests of Eucalyptus plantations worldwide. The egg parasitoid wasp
Anaphes nitens is used in many countries for the biological control of Gonipterus spp. Recent taxonomic
studies have shown that the three invasive Gonipterus spp., which were previously considered as
G. scutellatus, form part of a cryptic species complex. These taxonomic changes have implications
for the biological control of Gonipterus spp. The aims of this study were to understand the species
composition and distribution of Gonipterus spp. and their egg parasitoids in Australia. Gonipterus spp.
adults and egg capsules were collected in south-eastern Australia and Tasmania. Adult Gonipterus
were identified using morphology and DNA barcoding. Parasitoids were reared from Gonipterus
egg capsules and identified. Thirteen Gonipterus species were collected: twelve species were found
on the Australian mainland and one species in Tasmania. These included three described species,
four previously recognized but undescribed species, two undescribed species and four unidentified
species. Five egg parasitoid species that attack Gonipterus spp. were identified. Anaphes nitens,
Centrodora damoni and Euderus sp. were identified on the Australian mainland and A. tasmaniae
and A. inexpectatus were identified in Tasmania. The results from this study will contribute to the
improvement of Gonipterus biological control in the future.An Australia Awards Fellowship (Australian Department of Foreign Affairs and Trade), the University of the Sunshine Coast, South African Department of Science and Technology—Sector Specific Innovation Fund, the Tree-Protection Cooperative Programme (TPCP) at the Forestry and Agricultural Biotechnology Institute (FABI) of the University of Pretoria, Forest and Wood Products of Australia, and the Biological Control of Eucalypt Pests Alliance (BiCEP).https://www.mdpi.com/journal/forestsam2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyZoology and Entomolog
Metastatic Infiltration of Nervous Tissue and Periosteal Nerve Sprouting in Multiple Myeloma-Induced Bone Pain in Mice and Human
Multiple myeloma (MM) is a neoplasia of B plasma cells that often induces bone pain. However, the mechanisms underlying myeloma-induced bone pain (MIBP) are mostly unknown. Using a syngeneic MM mouse model, we show that periosteal nerve sprouting of calcitonin gene-related peptide (CGRP+) and growth associated protein 43 (GAP43+) fibers occurs concurrent to the onset of nociception and its blockade provides transient pain relief. MM patient samples also showed increased periosteal innervation. Mechanistically, we investigated MM induced gene expression changes in the dorsal root ganglia (DRG) innervating the MM-bearing bone of male mice and found alterations in pathways associated with cell cycle, immune response and neuronal signaling. The MM transcriptional signature was consistent with metastatic MM infiltration to the DRG, a never-before described feature of the disease that we further demonstrated histologically. In the DRG, MM cells caused loss of vascularization and neuronal injury, which may contribute to late-stage MIBP. Interestingly, the transcriptional signature of a MM patient was consistent with MM cell infiltration to the DRG. Overall, our results suggest that MM induces a plethora of peripheral nervous system alterations that may contribute to the failure of current analgesics and suggest neuroprotective drugs as appropriate strategies to treat early onset MIBP.SIGNIFICANCE STATEMENT Multiple myeloma (MM) is a painful bone marrow cancer that significantly impairs the quality of life of the patients. Analgesic therapies for myeloma-induced bone pain (MIBP) are limited and often ineffective, and the mechanisms of MIBP remain unknown. In this manuscript, we describe cancer-induced periosteal nerve sprouting in a mouse model of MIBP, where we also encounter metastasis to the dorsal root ganglia (DRG), a never-before described feature of the disease. Concomitant to myeloma infiltration, the lumbar DRGs presented blood vessel damage and transcriptional alterations, which may mediate MIBP. Explorative studies on human tissue support our preclinical findings. Understanding the mechanisms of MIBP is crucial to develop targeted analgesic with better efficacy and fewer side effects for this patient population
The Vehicle, Fall 1982
Vol. 24, No. 1
Table of Contents
Winter SurveillanceB.L. Davidsonpage 3
The InvitationBecky Lawsonpage 4
Check In, Check OutSteve Sandstrompage 4
On The Front Porch StepKeila Tooleypage 5
Old Greek ManDevon Flesorpage 5
Exotic PassionsBecky Lawsonpage 6
PhotographLisa Owenspage 7
Beyond The ThornsBrook Wilsonpage 8
Ritual Of HeatB.L. Davidsonpage 11
The GamerBecky Lawsonpage 12
It\u27s OverKeila Tooleypage 13
DreamJohn Stockmanpage 14
Silver DollarGina J. Grillopage 15
The DancerJessica Lewispage 16
Snapshots Of Rural IllinoisIsabel M. Parrottpage 16
The Last SeasonTheresa Whitesidepage 17
DrawingKaren Haneypage 17
Rotary LuncheonJessica Lewispage 18
Factory TourLinda Fraembspage 18
The ImmigrantsD.L. Lewispage 19
At Shedd AquariumLinda Fraembspage 20
The GuardianBecky Lewispage 20
Digital LifeEverett Tackettpage 21
Full ServiceScott Graypage 22
Dust ShowLinda A. Brownpage 23
At SixMaureen Foertschpage 24
DrawingJean Imherrpage 24
ReflectionMaggie Kennedypage 25
Cat DefiningBecky Lawsonpage 26
Ode To An Unread NewspaperLinda Fraembspage 26
GumSteve Sandstrompage 27
The DancerChrystal Clarkpage 27
PoemD.L. Lewispage 28
For LucyStacey Flanniganpage 29
An AbortionDevon Flesorpage 29
ReveriesKeila Tooleypage 30
Sunday Morning After Tequila With LemonScott Graypage 33
Staging A Living Jewel BoxMichelle Mitchellpage 34
The Other WomanStacey Flanniganpage 35
The Natural LookMichelle Mitchellpage 35
Poem To A Girl Named SandalsJohn Stockmanpage 36
PhotographLisa Owenspage 37
In The Balcony Of The Bijou On A Saturday NightScott Graypage 38
The Canadian Soccer PlayerBecky Lawsonpage 39
The HealingJohn Stockmanpage 39
AppeasedDevon Flesorpage 40
CodaJohn Stockmanpage 40https://thekeep.eiu.edu/vehicle/1040/thumbnail.jp
Development of a highly sensitive liquid biopsy platform to detect clinically-relevant cancer mutations at low allele fractions in cell-free DNA.
INTRODUCTION: Detection and monitoring of circulating tumor DNA (ctDNA) is rapidly becoming a diagnostic, prognostic and predictive tool in cancer patient care. A growing number of gene targets have been identified as diagnostic or actionable, requiring the development of reliable technology that provides analysis of multiple genes in parallel. We have developed the InVision™ liquid biopsy platform which utilizes enhanced TAm-Seq™ (eTAm-Seq™) technology, an amplicon-based next generation sequencing method for the identification of clinically-relevant somatic alterations at low frequency in ctDNA across a panel of 35 cancer-related genes. MATERIALS AND METHODS: We present analytical validation of the eTAm-Seq technology across two laboratories to determine the reproducibility of mutation identification. We assess the quantitative performance of eTAm-Seq technology for analysis of single nucleotide variants in clinically-relevant genes as compared to digital PCR (dPCR), using both established DNA standards and novel full-process control material. RESULTS: The assay detected mutant alleles down to 0.02% AF, with high per-base specificity of 99.9997%. Across two laboratories, analysis of samples with optimal amount of DNA detected 94% mutations at 0.25%-0.33% allele fraction (AF), with 90% of mutations detected for samples with lower amounts of input DNA. CONCLUSIONS: These studies demonstrate that eTAm-Seq technology is a robust and reproducible technology for the identification and quantification of somatic mutations in circulating tumor DNA, and support its use in clinical applications for precision medicine
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